Just wondering if it kicks players for clicking their mouse quick because a player said hes getting a message saying your spamming this too often, and he gets kicked just for picking up items from barrels, crates etc., here's a quick video.

Sure, Rust has a lot of commands that are hidden from the player and are executed during normal play (such as the "add" command).  It's necessary to identify these commands and add them to the white list.  If somone were to provide me with a list I would add them to the default list.

Warnings are printed to the console with a list of all the commands that offend the rate limiter, you can use these warning to identify which commands you want to white list.

Ive checked console and i don't see any warnings when he gets kicked, also when someone gets kicked it should say player getting kicked for spamming, or it just shows that he left the server ? how would i identify these commands, only by console ?

Enable LogExcessiveUsage.  The Kick Message is configurable in the language file.

spamming commands: lighttoggle 
spamming commands: respawn 
spamming commands: respawn_sleepingbag

some of the commands why they kept getting kicked.

Thank you, I'll add these to the default whitelist